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Horizontal gene transfer is an important means of bacterial evolution. This includes natural genetic transformation, where bacterial cells become “competent” and DNA is acquired from the extracellular environment. Natural competence in many species of  Streptococcus , is regulated by quorum sensing via the ComRS receptor-signal pair. The ComR-XIP (mature ComS peptide) complex induces expression of the alternative sigma factor SigX, which targets RNA polymerase to CIN-box promoters to activate genes involved in DNA uptake and recombination. In addition, the widely distributed  Streptococcus  prophage gene paratox ( prx ) also contains a CIN-box, and here we demonstrate it to be transcriptionally activated by XIP.  In vitro  experiments demonstrate that Prx binds ComR directly and prevents the ComR-XIP complex from interacting with DNA. Mutations of  prx in vivo  caused increased expression of the late competence gene  ssb  when induced with XIP as compared to wild-type, and Prx orthologues are able to inhibit ComR activation by XIP in a reporter strain which lacks an endogenous  prx . Additionally, an X-ray crystal structure of Prx reveals a unique fold that implies a novel molecular mechanism to inhibit ComR. Overall, our results suggest Prx functions to inhibit the acquisition of new DNA by  Streptococcus .

The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus